I would

1. scan all folders/files and create an array of them,
2. save this somewhere
3. run this scan again later [to check if the array still looks the same].

As you have the entire data structure from "time 1" and "now", you can clearly see what has changed. To crawl through the directories, check this: http://www.evoluted.net/thinktank/web-development/php-directory-listing-script

I would

1. scan all folders/files and create an array of them,
2. save this somewhere
3. run this scan again later [to check if the array still looks the same].

As you have the entire data structure from "time 1" and "now", you can clearly see what has changed. To crawl through the directories, check this: http://www.evoluted.net/thinktank/web-development/php-directory-listing-script and this http://phpmaster.com/list-files-and-directories-with-php/